Application startup time is slowed. On my system with Docker’s aufs backend it takes 2.5 seconds extra time for all applications, be it vim or iceweasel. I have read reports that on newer systems with SSDs and btrfs this can be reduced to a quarter of a second.

Certain things involving sharing of data between applications, like the clipboard in vim, just won’t work.

DBUS/gsettings don’t work between subusers.

Inheriting the $PWD is a generally shitty idea. If I run vim in my home dir, it can see and edit all of my files. The only security advantage is if I run vim in some subdirectory.

I hope this will be fixed by something more sophisticated like giving access only to paths specified in the command line arguments.

Disk usage is several times greater when installing one container per application due to the reduced ability to share dependencies

Docker will soon have ZFS support, which has limited support for block deduplication. Maybe future versions of Docker will have a venti based storage driver thus solving the problem perfectly and elegantly and also making updates even faster than on a traditional system.